There was, in fact, nothing wrong with Mr. Heicklen, 78, who eventually opened his eyes and told the judge, “I’m exercising my Fifth Amendment right to remain silent.”

Indeed, it was not his silence that landed Mr. Heicklen, a retired Pennsylvania State University chemistry professor, in court; it was what he had been doing outside the federal courthouse at 500 Pearl Street.

Since 2009, Mr. Heicklen has stood there and at courthouse entrances elsewhere and handed out pamphlets encouraging jurors to ignore the law if they disagree with it, and to render verdicts based on conscience.

That concept, called jury nullification, is highly controversial, and courts are hostile to it. But federal prosecutors have now taken the unusual step of having Mr. Heicklen indicted on a charge that his distributing of such pamphlets at the courthouse entrance violates a law against jury tampering.

Mr. Heicklen was arraigned on Friday in a somewhat contentious hearing before Judge Kimba M. Wood, who entered a not-guilty plea on Mr. Heicklen’s behalf when he refused to say how he would plead. During the proceeding, Mr. Heicklen railed at the judge and the government, and called the indictment “a tissue of lies.”

Mr. Heicklen insists that he never tries to influence specific jurors or cases, and instead gives his brochures to passers-by, hoping that jurors are among them.

But he feels his message must be getting out, or the government would not have brought charges against him.

“If I weren’t having any effect, would they do this?” said Mr. Heicklen, whose former colleagues recall him as a talented and unconventional educator. “You don’t have to be a genius to figure this thing out.”

Prosecutors declined to comment on his case, as did Sabrina Shroff, a lawyer who was assigned to assist Mr. Heicklen. (He is acting as his own lawyer.)

He said his activism on nullification dated back to just after he retired in the early 1990s, when he openly smoked marijuana in State College, Pa., to get arrested as a protest against marijuana laws. For this, he was arrested about five times. Mr. Heicklen has said that he otherwise does not smoke marijuana.

Around the same time, he learned about a group called the Fully Informed Jury Association, which urges jurors to nullify laws with which they disagree. Mr. Heicklen, of Teaneck, N.J., said he distributed the group’s materials as well as his own.

“I don’t want them to nullify the murder laws,” he said. “I’m a big law-and-order guy when it comes to real crime.”

But, he said, there were other laws he wanted to nullify, like drug and gambling laws.

“This is classic political advocacy,” Christopher T. Dunn, associate legal director of the New York Civil Liberties Union, said of Mr. Heicklen’s pamphleteering. “Unless the government can show that he’s singling out jurors to influence a specific verdict, it’s squarely protected by the First Amendment, and they should dismiss the case.”

But Daniel C. Richman, a former prosecutor who teaches criminal law at Columbia, said there was an interest in ensuring the integrity of the jury process. “The government has to walk a fine First Amendment line bringing these charges,” he said, “but lawless jury behavior is certainly of concern to it, too.”

Mr. Heicklen says that when he stands outside the court, he holds a sign that reads “Jury Info” to draw people to him. “Sometimes they think I’m official,” he said. He answers questions and advises that jurors have the right to nullify.

Jessica A. Roth, a Cardozo law professor and a former prosecutor, said such activities could confuse and mislead jurors, since “the information he’s giving these people is likely to be in direct conflict with the instructions they will receive from a judge if they are jurors in a case.”

Mr. Heicklen, a Cornell graduate, taught for more than 20 years at Penn State, where he was a faculty member known for his innovative methods, former colleagues said.

Mr. Heicklen would bring Penn State dancers, actors and cheerleaders into one course to illustrate molecular vibration and to celebrate scientific discovery. “People talked about this course for years,” Robert Bernheim, a retired professor, recalled.

Barbara J. Garrison, who heads the Penn State chemistry department, called Mr. Heicklen “an enormously creative scientist” who “really liked to think outside the box and sometimes that meant that he ran counter to the establishment.”

About his earlier marijuana arrests, Ms. Garrison said, “He had his own way of doing it, but he was really fighting for people who were in jail that he didn’t think belonged in jail.”

Court records show that before Mr. Heicklen’s indictment last fall, he had been cited at least six times since October 2009 for distributing fliers without a permit at the entrance of the Manhattan federal courthouse. But the violations, which carry fines, do not depend on the content of his message. If convicted of trying to improperly influence jurors, he could face a six-month sentence.

When issued a citation, Mr. Heicklen said, he sometimes intentionally dropped to the sidewalk and had even been taken to local hospitals, where he was examined and released.

In court on Friday, Judge Wood cited a written request by Mr. Heicklen that Muslims be “excluded from the jury” because he was Jewish and “Islam preaches death to Jews.” Because he was charged with a misdemeanor, she said, he was not entitled to a jury trial; and in any case, she said, jurors may not be excluded because of religion.

Mr. Heicklen has extended his protest to suing the government and various hospitals to which he was taken after being issued citations and falling to the ground.

“Plaintiff Heicklen,” he said in one suit, “has become an angry man.”

A version of this article appeared in print on February 26, 2011, on page A17 of the New York edition.